GO DATABASE DOWNLOADS
=====================
For full documentation see
http://www.geneontology.org/GO.database.shtml
FILENAME CONVENTION
===================
releases are named
go_<YYYYMM>-<DATASET><TYPE>
YYYYMM is the release date (the release export usually follows some
time after the monthly release, due to time taken to build)
the DATASET is one of:
-------
* termdb - a database containing just the information on the
GO terms and relationships. These are the table that are populated:
term GO controlled vocab terms
term2term relationships between GO terms
term_definition definitions of terms
dbxref external database identifier entities
term_dbxref links from terms to other databases
term_synonym synonyms for terms
graph_path transitive closure (all paths) in graph
* assocdb - a database containing both the GO vocabulary and
associations between GO terms and gene products. This database
subsumes termdb. These are the extra tables that are populated:
gene_product gene or protein or entity annotated
association link between gene product and GO term
evidence evidence type and reference for an assoc
gene_product_count recursive product counts per GO term
*seqdb - a database containing GO terms, gene products and the
sequences associated with these gene products. This db subsumes the
two above. It populates these additional tables:
seq biological sequence
gene_product_seq link between a product and a sequence
seq_dbxref external database links for a sequence
NOTE: there are other unpopulated tables - we may or may not decide to
populate these at some point in the future.
*seqdblite - this is the same as seqdb, except all IEA associations
have been removed. The IEA associations provide relatively little
value compared to the curated associations, and they slow querying
down immensely. This is the distribution that AmiGO runs off of. We
are working on optimisations to allow AmiGO to run off of the full
seqdb release.
the TYPE is either
----
.rdf-xml - RDF XML export of the database. this comes as one single
file. Note there is no RDF XML export of seqdb, as we do not include
sequences in the xml yet. We do not include IEA evidence associations
in the xml. We may decide to split this xml file into multiple files
at a later date.
.obo-xml - OBO XML Export. Currently ontology only
.owl - OWL Export. Currently ontology only
.tables - this is a directory containing the MySQL dump, see below
.sql - SQL CREATE TABLE and INSERT statements for building a local
instance of the database. equivalent to the .tables TYPE (but slower
to load)
SCHEMA DOCUMENTATION
********************
### The schema file is no longer being provided as of 2011-01-27
In this distribution, uncompreess the file:
go_YYYYMM-schema-mysql.sql.gz
Which contains the (MySQL ported) schema used in this release
You can also look at the HTML marked up version of the schema, or
schema diagrams here:
Go to
http://www.geneontology.org/GO.database.shtml
click on "Schema Docs" or "Tables" in the sidebar
To guarantee that your schema, code and database release are in sync
you should use the files from the same release.
**********************************
MYSQL USERS
The database export was prepared from a mysql db - you should have no
problem importing it:
tar -zxvf go-YYYYMM-TYPE-tables.gz
cd <releasedir>
echo "create database mygo" | mysql
cat *.sql | mysql mygo
mysqlimport -L mygo *.txt
Note: if you are using Windows, you may see warning messages when
loading some tables; to avoid this, load tables this way:
mysql> load data infile
"c:\\download\\GO\\july-release\\go_200307-assocdb-table
s\\association.txt" into table association lines terminated by '\r\n';
This can be avoided if you disable "TAR file smart CR/LF conversion"
when using Winzip (thanks to Henrik Edgren for the tip
We are unable to support Windows users - please refer to your MySQL
documentation; if you experience other problems, you may wish to try
posting a question to the go-database mail list to see if other
Windows users have any advice.
**********************************
OTHER DBMS USERS
Your database is not supported; but we do have some tips below:
also: the perl api code is mostly DBMS neutral, it should in theory
work on non mysql setups
**********************************
POSTGRES USERS:
TIP: for converting mysql dumps to postgres, try my2pg
http://www.ziet.zhitomir.ua/~fonin/code/
Thanks to Joe Morris of Affymetrix for the tip
************************************
ORACLE USERS:
see the directory sql/oracle/ in the go_YYYYMM-utilities_src software
distribution
This is contributed software, and not supported by the go-dev group.
************************************
PROGRAMMERS:
you can access the data using the perl API - see
http://www.geneontology.org/GO.database.shtml
OR look at the perl API release for the data release:
tar -zxvf go_YYYYMM-utilities_src.tar.gz
cd go_YYYYMM-utilities_src
cd perl-api
perldoc GO/AppHandle.pm
sometimes the perl API must be in sync with the database, eg if the
schema changes in a way to break old code
*************************************
AMIGO:
you can build a local AmiGO installation using the source code and
data included in this distribution. You can load your own data into it
using either the scripts in go-dev/apps/db-loading, or the configure
script and makefile in go-dev/sql
*************************************
QUESTIONS:
Email the go-database mail list; go to
http://www.geneontology.org/GO.database.shtml
And click on "Mail List" in the sidebar
Be sure to have read the rest of the database documentation before
asking a question